Apple won't be fixing this. Their approach is to recommend transit apps depending on your location instead.
Now if only you could change the default handler for addresses to route to other mapping/direction programs. Once we get that, this teapot tempest will die out.
Carriers already push iPhone alternatives for all sorts of reasons. It doesn't matter how good the third-party transit apps are. Not having transit routing built in is an "instant demo" for any carrier sales rep trying to push an Android or Windows Phone. And, last I heard, Apple sells far more iPhones through carriers that they sell directly...